[Bioperl-l] trouble to retrieve sequence.. I'm a BEGINNER...

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Tue Dec 6 01:28:00 EST 2005


> Thank you for your help.
> I solved the problem by installing IO:String module...but
> there are another problems like this;
> ------------- EXCEPTION  -------------
> MSG: Error from Genbank: Your query produced warning/error messages - check flagged link below.
> STACK Bio::DB::Query::GenBank::_parse_response /usr/lib/perl5/site_perl/5.6.0/Bio/DB/Query/GenBank.pm:267
> STACK Bio::DB::Query::WebQuery::_run_query /usr/lib/perl5/site_perl/5.6.0/Bio/DB/Query/WebQuery.pm:268
> STACK Bio::DB::Query::GenBank::cookie /usr/lib/perl5/site_perl/5.6.0/Bio/DB/Query/GenBank.pm:177
> STACK Bio::DB::NCBIHelper::get_request /usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm:187
> STACK Bio::DB::WebDBSeqI::get_seq_stream /usr/lib/perl5/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm:438
> STACK Bio::DB::NCBIHelper::get_Stream_by_query /usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm:248
> STACK toplevel query.pl:12
> Could you help me one more time, please?

It seems the MSG: line says that your Genbank query was invalid.

Your original query was:
$query = "Arabidopsis[ORGN] AND topoisomerase[TITL] an 0:3000[SLEN]";

Should that be " AND 0:3000[SLEN]" ?

Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
Victorian Bioinformatics Consortium

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